PetscSolverGlobalMatrix.cc 26.8 KB
Newer Older
Thomas Witkowski's avatar
Thomas Witkowski committed
1 2 3 4 5 6 7 8 9 10 11
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.

12 13
#include <mpi.h>
#include "DirichletBC.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
14 15 16 17 18 19
#include "parallel/PetscSolverGlobalMatrix.h"
#include "parallel/StdMpi.h"
#include "parallel/MpiHelper.h"

namespace AMDiS {

20 21 22 23 24 25 26 27 28 29 30

  PetscSolverGlobalMatrix::PetscSolverGlobalMatrix(string name)
    : PetscSolver(name),
      zeroStartVector(false),
      printMatInfo(false)
  {
    Parameters::get("parallel->use zero start vector", zeroStartVector);
    Parameters::get("parallel->print matrix info", printMatInfo);
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
31
  void PetscSolverGlobalMatrix::fillPetscMatrix(Matrix<DOFMatrix*> *seqMat)
Thomas Witkowski's avatar
Thomas Witkowski committed
32 33 34
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
35 36 37 38 39 40
    TEST_EXIT_DBG(meshDistributor)("No mesh distributor object defined!\n");
    TEST_EXIT_DBG(interiorMap)("No parallel mapping object defined!\n");
    TEST_EXIT_DBG(seqMat)("No DOF matrix defined!\n");
    
    double wtime = MPI::Wtime();

41
    createMatVec(*seqMat);
42

Thomas Witkowski's avatar
Thomas Witkowski committed
43
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
44
      fillPetscMatrixWithCoarseSpace(seqMat);
45 46
      return;
    }
47
    
48 49
    // === Create PETSc vector (solution and a temporary vector). ===

Thomas Witkowski's avatar
Thomas Witkowski committed
50 51 52 53 54 55
#if (DEBUG != 0)
    MSG("Fill petsc matrix 1 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

    // === Transfer values from DOF matrices to the PETSc matrix. === 

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
56
    int nComponents = seqMat->getNumRows();
Thomas Witkowski's avatar
Thomas Witkowski committed
57 58
    for (int i = 0; i < nComponents; i++)
      for (int j = 0; j < nComponents; j++)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
59 60
	if ((*seqMat)[i][j])
	  setDofMatrix((*seqMat)[i][j], i, j);
Thomas Witkowski's avatar
Thomas Witkowski committed
61 62 63 64 65

#if (DEBUG != 0)
    MSG("Fill petsc matrix 2 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif

66
    matAssembly();
67

68 69
    if (printMatInfo) {
      MatInfo matInfo;
70
      MatGetInfo(getMatInterior(), MAT_GLOBAL_SUM, &matInfo);
71 72 73 74 75 76 77
      MSG("Matrix info:\n");
      MSG("  memory usage: %e MB\n", matInfo.memory / (1024.0 * 1024.0));
      MSG("  mallocs: %d\n", static_cast<int>(matInfo.mallocs));
      MSG("  nz allocated: %d\n", static_cast<int>(matInfo.nz_allocated));
      MSG("  nz used: %d\n", static_cast<int>(matInfo.nz_used));
      MSG("  nz unneeded: %d\n", static_cast<int>(matInfo.nz_unneeded));
    }
78 79


80
    // === Init PETSc solver and preconditioner objects. ===
81

82 83
    initSolver(kspInterior);
    KSPGetPC(kspInterior, &pcInterior);
84
    initPreconditioner(pcInterior);
85

86

Thomas Witkowski's avatar
Thomas Witkowski committed
87 88 89
#if (DEBUG != 0)
    MSG("Fill petsc matrix 3 needed %.5f seconds\n", MPI::Wtime() - wtime);
#endif
90 91


92 93 94 95 96 97 98 99 100 101 102
    // === For debugging allow to write the matrix to a file. ===

    bool dbgWriteMatrix = false;
    Parameters::get("parallel->debug->write matrix", dbgWriteMatrix);
    if (dbgWriteMatrix) {
      PetscViewer matView;
      PetscViewerBinaryOpen(PETSC_COMM_WORLD, "mpi.mat",
			    FILE_MODE_WRITE, &matView);
      MatView(getMatInterior(), matView);
      PetscViewerDestroy(&matView);
    }
103 104 105
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
106
  void PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace(Matrix<DOFMatrix*> *seqMat)
107 108
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
109 110

    TEST_EXIT_DBG(interiorMap)("Should not happen!\n");
111 112
    TEST_EXIT_DBG(coarseSpaceMap.size() == seqMat->getSize())
      ("Wrong sizes %d %d\n", coarseSpaceMap.size(), seqMat->getSize());
113

114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129
    // === Prepare traverse of sequentially created matrices. ===

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
    namespace traits = mtl::traits;
    typedef DOFMatrix::base_matrix_type Matrix;

    typedef traits::range_generator<row, Matrix>::type cursor_type;
    typedef traits::range_generator<nz, cursor_type>::type icursor_type;

    vector<int> cols, colsOther;
    vector<double> values, valuesOther;
    cols.reserve(300);
    colsOther.reserve(300);
    values.reserve(300);
    valuesOther.reserve(300);

130 131 132
    bool localMatrix = 
      (meshDistributor->getMeshLevelData().getMpiComm(meshLevel) == MPI::COMM_SELF);

133 134 135
    // === Traverse all sequentially created matrices and add the values to ===
    // === the global PETSc matrices.                                       ===

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
136
    int nComponents = seqMat->getSize();
Thomas Witkowski's avatar
Thomas Witkowski committed
137 138 139 140 141
    for (int rowComponent = 0; rowComponent < nComponents; rowComponent++) {
      for (int colComponent = 0; colComponent < nComponents; colComponent++) {
	DOFMatrix* dofMat = (*seqMat)[rowComponent][colComponent];

	if (!dofMat)
142 143
	  continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
144 145
	ParallelDofMapping *rowCoarseSpace = coarseSpaceMap[rowComponent];
	ParallelDofMapping *colCoarseSpace = coarseSpaceMap[colComponent];
Thomas Witkowski's avatar
Thomas Witkowski committed
146

Thomas Witkowski's avatar
Thomas Witkowski committed
147 148
	std::set<DegreeOfFreedom> &dirichletRows = dofMat->getDirichletRows();

Thomas Witkowski's avatar
Thomas Witkowski committed
149 150
	traits::col<Matrix>::type col(dofMat->getBaseMatrix());
	traits::const_value<Matrix>::type value(dofMat->getBaseMatrix());
151 152
	
	// Traverse all rows.
Thomas Witkowski's avatar
Thomas Witkowski committed
153 154
	for (cursor_type cursor = begin<row>(dofMat->getBaseMatrix()), 
	       cend = end<row>(dofMat->getBaseMatrix()); cursor != cend; ++cursor) {
155

Thomas Witkowski's avatar
Thomas Witkowski committed
156
	  bool isRowCoarse = isCoarseSpace(rowComponent, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
157 158 159 160 161 162

	  // For the case, this is a dirichlet row we have to check whether the 
	  // rank is also owner of this row DOF.
	  if (dirichletRows.count(*cursor)) {
	    if ((!isRowCoarse && !(*interiorMap)[rowComponent].isRankDof(*cursor)) ||
		(isRowCoarse && !(*rowCoarseSpace)[rowComponent].isRankDof(*cursor)))
163
	      continue;    
Thomas Witkowski's avatar
Thomas Witkowski committed
164
	  }
165 166 167 168 169 170 171 172 173 174
  
	  cols.clear();
	  colsOther.clear();
	  values.clear();	  
	  valuesOther.clear();

	  // Traverse all columns.
	  for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	       icursor != icend; ++icursor) {

Thomas Witkowski's avatar
Thomas Witkowski committed
175
	    bool isColCoarse = isCoarseSpace(colComponent, col(*icursor));
176

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
177
	    if (isColCoarse == false)
178
	      if ((*interiorMap)[colComponent].isSet(col(*icursor)) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
179 180
		continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
181 182 183
	    if (isColCoarse == isRowCoarse) {
	      cols.push_back(col(*icursor));
	      values.push_back(value(*icursor));
184
	    } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
185 186
	      colsOther.push_back(col(*icursor));
	      valuesOther.push_back(value(*icursor));
187 188 189 190 191 192
	    }
	  }  // for each nnz in row


	  // === Set matrix values. ===

Thomas Witkowski's avatar
Thomas Witkowski committed
193
	  if (isRowCoarse) {
Thomas Witkowski's avatar
Thomas Witkowski committed
194 195
	    for (unsigned int i = 0; i < cols.size(); i++)
	      cols[i] = colCoarseSpace->getMatIndex(colComponent, cols[i]);
196

Thomas Witkowski's avatar
Thomas Witkowski committed
197
	    int rowIndex = rowCoarseSpace->getMatIndex(rowComponent, *cursor);
Thomas Witkowski's avatar
Thomas Witkowski committed
198
	    MatSetValues(getMatCoarseByComponent(rowComponent, colComponent),
199 200
	    		 1, &rowIndex, cols.size(),
	    		 &(cols[0]), &(values[0]), ADD_VALUES);
201 202

	    if (colsOther.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
203 204 205
	      for (unsigned int i = 0; i < colsOther.size(); i++)
		colsOther[i] = 
		  interiorMap->getMatIndex(colComponent, colsOther[i]) + 
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
206
		  rStartInterior;	      
207

Thomas Witkowski's avatar
Thomas Witkowski committed
208
	      MatSetValues(getMatCoarseInteriorByComponent(rowComponent), 
209 210
	       		   1, &rowIndex, colsOther.size(),
 	       		   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
211 212
	    }
	  } else {
213
	    if ((*interiorMap)[rowComponent].isSet(*cursor) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
214 215
	      continue;

216
	    int localRowIndex = 
217
	      (localMatrix ? 
Thomas Witkowski's avatar
Thomas Witkowski committed
218 219
	       interiorMap->getLocalMatIndex(rowComponent, *cursor) :
	       interiorMap->getMatIndex(rowComponent, *cursor));
220

Thomas Witkowski's avatar
Thomas Witkowski committed
221
	    for (unsigned int i = 0; i < cols.size(); i++) {
222
	      if (localMatrix)
Thomas Witkowski's avatar
Thomas Witkowski committed
223
		cols[i] = interiorMap->getLocalMatIndex(colComponent, cols[i]);
224
	      else
Thomas Witkowski's avatar
Thomas Witkowski committed
225
		cols[i] = interiorMap->getMatIndex(colComponent, cols[i]);
226 227
	    }
	    
228 229
	    MatSetValues(getMatInterior(), 1, &localRowIndex, cols.size(),
  	     		 &(cols[0]), &(values[0]), ADD_VALUES);
Thomas Witkowski's avatar
Thomas Witkowski committed
230
	    
231
	    if (colsOther.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
232 233 234
	      int globalRowIndex = 
		interiorMap->getMatIndex(rowComponent, *cursor) + rStartInterior;
      
Thomas Witkowski's avatar
Thomas Witkowski committed
235 236 237
	      for (unsigned int i = 0; i < colsOther.size(); i++)
		colsOther[i] = 
		  colCoarseSpace->getMatIndex(colComponent, colsOther[i]);
238

239 240 241
	      MatSetValues(getMatInteriorCoarseByComponent(colComponent), 
			   1, &globalRowIndex, colsOther.size(),
			   &(colsOther[0]), &(valuesOther[0]), ADD_VALUES);
242 243 244 245 246 247
	    }
	  }
	} 
      }
    }

248
    matAssembly();
249

250 251
    // === Create solver for the non primal (thus local) variables. ===

252
    KSPCreate(domainComm, &kspInterior);
253
    KSPSetOperators(kspInterior, getMatInterior(), getMatInterior(),
254
		    SAME_NONZERO_PATTERN);
255 256 257
    KSPSetOptionsPrefix(kspInterior, "interior_");
    KSPSetType(kspInterior, KSPPREONLY);
    KSPGetPC(kspInterior, &pcInterior);
258 259
    if (isSymmetric) {
      PCSetType(pcInterior, PCCHOLESKY);
260
      PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
261 262
    } else {
      PCSetType(pcInterior, PCLU);
263
      if (localMatrix)
264 265 266 267
	PCFactorSetMatSolverPackage(pcInterior, MATSOLVERUMFPACK);
      else
	PCFactorSetMatSolverPackage(pcInterior, MATSOLVERMUMPS);
    }
268
    KSPSetFromOptions(kspInterior);
269 270 271
  }


272 273 274
  void PetscSolverGlobalMatrix::fillPetscRhs(SystemVector *vec)
  {
    FUNCNAME("PetscSolverGlobalMatrix::fillPetscRhs()");
Thomas Witkowski's avatar
Thomas Witkowski committed
275

276
    TEST_EXIT_DBG(vec)("No DOF vector defined!\n");
277
    TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
278
    
Thomas Witkowski's avatar
Thomas Witkowski committed
279
    // === Transfer values from DOF vector to the PETSc vector. === 
Thomas Witkowski's avatar
Thomas Witkowski committed
280
    if (coarseSpaceMap.size()) {
Thomas Witkowski's avatar
Thomas Witkowski committed
281
      for (int i = 0; i < vec->getSize(); i++)
282
	setDofVector(getVecRhsInterior(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
283
		     getVecRhsCoarseByComponent(i), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
284 285
    } else {
      for (int i = 0; i < vec->getSize(); i++)
286
	setDofVector(getVecRhsInterior(), vec->getDOFVector(i), i);
Thomas Witkowski's avatar
Thomas Witkowski committed
287 288
    }

289
    vecRhsAssembly();
290 291 292 293 294 295 296 297 298 299 300 301

    // === For debugging allow to write the rhs vector to a file. ===

    bool dbgWriteRhs = false;
    Parameters::get("parallel->debug->write rhs", dbgWriteRhs);
    if (dbgWriteRhs) {
      PetscViewer vecView;
      PetscViewerBinaryOpen(PETSC_COMM_WORLD, "mpi.vec",
			    FILE_MODE_WRITE, &vecView);
      VecView(getVecRhsInterior(), vecView);
      PetscViewerDestroy(&vecView);
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
302 303 304
  }


305 306
  void PetscSolverGlobalMatrix::solvePetscMatrix(SystemVector &vec, 
						 AdaptInfo *adaptInfo)
Thomas Witkowski's avatar
Thomas Witkowski committed
307 308 309 310 311 312 313
  {
    FUNCNAME("PetscSolverGlobalMatrix::solvePetscMatrix()");

    int nComponents = vec.getSize();

    // === Set old solution to be initiual guess for PETSc solver. ===
    if (!zeroStartVector) {
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
314 315
      TEST_EXIT(coarseSpaceMap.size() == 0)("Not yet supported!\n");

316
      VecSet(getVecSolInterior(), 0.0);
Thomas Witkowski's avatar
Thomas Witkowski committed
317 318
      
      for (int i = 0; i < nComponents; i++)
319
	setDofVector(getVecSolInterior(), vec.getDOFVector(i), i, true);
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
320

321
      vecSolAssembly();
Thomas Witkowski's avatar
Thomas Witkowski committed
322 323
    }

324

Thomas Witkowski's avatar
Thomas Witkowski committed
325 326
    MatNullSpace matNullspace;
    Vec nullspaceBasis;
327 328 329
    if (nullspace.size() > 0 || 
	hasConstantNullspace ||
	constNullspaceComponent.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
330
      TEST_EXIT_DBG(nullspace.size() <= 1)("Not yet implemented!\n");
331

332 333 334 335 336 337 338 339 340 341
      if (constNullspaceComponent.size() > 0) {
	nullspace.clear();
	SystemVector *basisVec = new SystemVector(vec);
	basisVec->set(0.0);
	for (unsigned int i = 0; i < constNullspaceComponent.size(); i++)
	  basisVec->getDOFVector(constNullspaceComponent[i])->set(1.0);

	nullspace.push_back(basisVec);
      } 

Thomas Witkowski's avatar
Thomas Witkowski committed
342
      if (nullspace.size() > 0) {
343
	VecDuplicate(getVecSolInterior(), &nullspaceBasis);
344
	setDofVector(nullspaceBasis, *(nullspace[0]), true);
Thomas Witkowski's avatar
Thomas Witkowski committed
345 346 347
	
	VecAssemblyBegin(nullspaceBasis);
	VecAssemblyEnd(nullspaceBasis);
348 349

	VecNormalize(nullspaceBasis, PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
350
	
351
	MatNullSpaceCreate(domainComm, (hasConstantNullspace ? PETSC_TRUE : PETSC_FALSE), 
Thomas Witkowski's avatar
Thomas Witkowski committed
352 353
			   1, &nullspaceBasis, &matNullspace);

354
	MatMult(getMatInterior(), nullspaceBasis, getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
355
	PetscReal n;
356
	VecNorm(getVecSolInterior(), NORM_2, &n);
Thomas Witkowski's avatar
Thomas Witkowski committed
357 358
	MSG("NORM IS: %e\n", n);
      } else {
359
	MatNullSpaceCreate(domainComm, PETSC_TRUE, 0, PETSC_NULL, &matNullspace);
Thomas Witkowski's avatar
Thomas Witkowski committed
360
      }
361

Thomas Witkowski's avatar
Thomas Witkowski committed
362 363 364
      MSG("NULLSPACE IS NOT REMOVED!\n");
      // MatSetNullSpace(getMatInterior(), matNullspace);
      // KSPSetNullSpace(kspInterior, matNullspace);
365

Thomas Witkowski's avatar
Thomas Witkowski committed
366
      // === Remove null space, if requested. ===
367

Thomas Witkowski's avatar
Thomas Witkowski committed
368
      if (removeRhsNullspace) {
Thomas Witkowski's avatar
Thomas Witkowski committed
369
	TEST_EXIT_DBG(coarseSpaceMap.empty())("Not supported!\n");
370 371

	MSG("Remove nullspace from rhs vector.\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
372
	
373
	MatNullSpaceRemove(matNullspace, getVecRhsInterior(), PETSC_NULL);
Thomas Witkowski's avatar
Thomas Witkowski committed
374 375 376 377
      }
    } else {
      TEST_EXIT(removeRhsNullspace == false)
	("No nullspace provided that should be removed from rhs!\n");
378 379
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
380
    // PETSc.
381
    solve(getVecRhsInterior(), getVecSolInterior());
Thomas Witkowski's avatar
Thomas Witkowski committed
382

383 384

    if (nullspace.size() > 0) {
Thomas Witkowski's avatar
Thomas Witkowski committed
385
      MatNullSpaceDestroy(&matNullspace);
386 387 388 389
      VecDestroy(&nullspaceBasis);
    }


Thomas Witkowski's avatar
Thomas Witkowski committed
390 391
    // === Transfere values from PETSc's solution vectors to the DOF vectors. ===
    PetscScalar *vecPointer;
392
    VecGetArray(getVecSolInterior(), &vecPointer);    
Thomas Witkowski's avatar
Thomas Witkowski committed
393

394
    int c = 0;
395 396
    for (int component = 0; component < nComponents; component++) {
      DOFVector<double> &dv = *(vec.getDOFVector(component));
397

398
      DofMap& d = (*interiorMap)[component].getMap();
399 400 401
      for (DofMap::iterator it = d.begin(); it != d.end(); ++it)
	if (it->second.local != -1)
	  dv[it->first] = vecPointer[c++];
Thomas Witkowski's avatar
Thomas Witkowski committed
402 403
    }

404
    VecRestoreArray(getVecSolInterior(), &vecPointer);
Thomas Witkowski's avatar
Thomas Witkowski committed
405 406 407 408

    // === Synchronize DOFs at common DOFs, i.e., DOFs that correspond to ===  
    // === more than one partition.                                       ===  
    meshDistributor->synchVector(vec);
409 410 411
  }


412 413 414 415
  void PetscSolverGlobalMatrix::solveGlobal(Vec &rhs, Vec &sol)
  {
    FUNCNAME("PetscSolverGlobalMatrix::solveGlobal()");

416 417 418
    double wtime = MPI::Wtime();
    double t0 = 0.0, t1 = 0.0;

419
    Vec tmp;
420
    if (domainComm.Get_size() == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
421
      interiorMap->createLocalVec(tmp);
422
    else
Thomas Witkowski's avatar
Thomas Witkowski committed
423
      interiorMap->createVec(tmp);
424 425 426 427 428 429 430 431 432 433 434

    PetscScalar *tmpValues, *rhsValues;
    VecGetArray(tmp, &tmpValues);
    VecGetArray(rhs, &rhsValues);

    for (int i = 0; i < interiorMap->getRankDofs(); i++)
      tmpValues[i] = rhsValues[i];

    VecRestoreArray(rhs, &rhsValues);
    VecRestoreArray(tmp, &tmpValues);

435 436 437
    t0 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
438
    KSPSolve(kspInterior, tmp, tmp);
439 440 441
    t1 = MPI::Wtime() - wtime;

    wtime = MPI::Wtime();
442 443 444 445 446 447 448 449 450 451 452

    VecGetArray(tmp, &tmpValues);
    VecGetArray(sol, &rhsValues);

    for (int i = 0; i < interiorMap->getRankDofs(); i++) 
      rhsValues[i] = tmpValues[i];

    VecRestoreArray(sol, &rhsValues);
    VecRestoreArray(tmp, &tmpValues);

    VecDestroy(&tmp);
453 454
    t0 += MPI::Wtime() - wtime;

455
    //    MSG("TIMEING: %.5f %.5f\n", t0, t1);
456 457 458
  }


459 460 461 462
  void PetscSolverGlobalMatrix::destroyMatrixData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyMatrixData()");

463
    matDestroy();
Thomas Witkowski's avatar
Thomas Witkowski committed
464

465 466 467
    exitPreconditioner(pcInterior);

    exitSolver(kspInterior);
Thomas Witkowski's avatar
Thomas Witkowski committed
468 469 470
  }


471 472 473 474
  void PetscSolverGlobalMatrix::destroyVectorData()
  {
    FUNCNAME("PetscSolverGlobalMatrix::destroyVectorData()");

475
    vecDestroy();
476 477 478
  }


479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497
  void PetscSolverGlobalMatrix::createFieldSplit(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createFieldSplit()");

    vector<string> isNames;
    Parameters::get("parallel->solver->is blocks", isNames);

    int nBlocks = isNames.size();
    if (nBlocks == 0)
      return;

    for (int i = 0; i < nBlocks; i++) {
      MSG("Create for block %s\n", isNames[i].c_str());

      vector<int> blockComponents;
      Parameters::get("parallel->solver->is block " + lexical_cast<string>(i),
		      blockComponents);
      int nComponents = static_cast<int>(blockComponents.size());

498
      TEST_EXIT(nComponents > 0)("No IS block for block %d defined!\n", i);
499 500 501 502 503 504 505 506

      // Check if blocks are continous
      for (int j = 0; j < nComponents; j++) {
	TEST_EXIT(blockComponents[j] == blockComponents[0] + j)
	  ("Does not yet support not continous IS blocks! Block %s\n", 
	   isNames[i].c_str());
      }

507
      createFieldSplit(pc, isNames[i].c_str(), blockComponents);
508 509 510 511
    }
  }


512
  void PetscSolverGlobalMatrix::createFieldSplit(PC pc, 
513
						 const char* splitName, 
514 515 516 517 518 519
						 vector<int> &components)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createFieldSplit()");

    IS is;
    interiorMap->createIndexSet(is, components[0], components.size());
520
    PCFieldSplitSetIS(pc, splitName, is);
521 522 523 524
    ISDestroy(&is);
  }


525
  void PetscSolverGlobalMatrix::initSolver(KSP &ksp)
526 527 528
  {
    FUNCNAME("PetscSolverGlobalMatrix::initSolver()");

529
    KSPCreate(domainComm, &ksp);
530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550
    KSPSetOperators(ksp, getMatInterior(), getMatInterior(), 
		    SAME_NONZERO_PATTERN); 
    KSPSetTolerances(ksp, 0.0, 1e-8, PETSC_DEFAULT, PETSC_DEFAULT);
    KSPSetType(ksp, KSPBCGS);
    KSPSetOptionsPrefix(ksp, kspPrefix.c_str());
    KSPSetFromOptions(ksp);

    // Do not delete the solution vector, use it for the initial guess.
    if (!zeroStartVector)
      KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
  }  


  void PetscSolverGlobalMatrix::exitSolver(KSP ksp)
  {
    FUNCNAME("PetscSolverGlobalMatrix::exitSolver()");

    KSPDestroy(&ksp);
  }  


551 552 553 554 555 556 557 558 559 560 561 562 563 564 565
  void PetscSolverGlobalMatrix::initPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::initPreconditioner()");

    PCSetFromOptions(pc);
    createFieldSplit(pc);
  }

 
  void PetscSolverGlobalMatrix::exitPreconditioner(PC pc)
  {
    FUNCNAME("PetscSolverGlobalMatrix::exitPreconditioner()");
  }


Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
566
  void PetscSolverGlobalMatrix::setDofMatrix(DOFMatrix* seqMat,
Thomas Witkowski's avatar
Thomas Witkowski committed
567
					     int rowComp, int colComp)
Thomas Witkowski's avatar
Thomas Witkowski committed
568 569 570
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofMatrix()");

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
571
    TEST_EXIT(seqMat)("No DOFMatrix!\n");
Thomas Witkowski's avatar
Thomas Witkowski committed
572 573

    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
574
    namespace traits = mtl::traits;
Thomas Witkowski's avatar
Thomas Witkowski committed
575 576
    typedef DOFMatrix::base_matrix_type Matrix;

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
577 578
    traits::col<Matrix>::type col(seqMat->getBaseMatrix());
    traits::const_value<Matrix>::type value(seqMat->getBaseMatrix());
Thomas Witkowski's avatar
Thomas Witkowski committed
579 580 581 582 583 584 585 586 587 588 589

    typedef traits::range_generator<row, Matrix>::type cursor_type;
    typedef traits::range_generator<nz, cursor_type>::type icursor_type;

    vector<int> cols;
    vector<double> values;
    cols.reserve(300);
    values.reserve(300);
    
    vector<int> globalCols;

590 591
    // Get periodic mapping object
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Thomas Witkowski committed
592 593
    std::set<DegreeOfFreedom> &dirichletRows = seqMat->getDirichletRows();
      
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
594 595
    const FiniteElemSpace *rowFe = seqMat->getRowFeSpace();
    const FiniteElemSpace *colFe = seqMat->getColFeSpace();
Thomas Witkowski's avatar
Thomas Witkowski committed
596 597

    // === Traverse all rows of the DOF matrix and insert row wise the values ===
Thomas Witkowski's avatar
Thomas Witkowski committed
598 599
    // === to the PETSc matrix.                                               ===

Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
600 601
    for (cursor_type cursor = begin<row>(seqMat->getBaseMatrix()), 
	   cend = end<row>(seqMat->getBaseMatrix()); cursor != cend; ++cursor) {
Thomas Witkowski's avatar
Thomas Witkowski committed
602
      // Global index of the current row DOF.
603
      MultiIndex rowMultiIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
604
      if ((*interiorMap)[rowComp].find(*cursor, rowMultiIndex) == false)
605 606 607
	continue;

      int globalRowDof = rowMultiIndex.global;
608

Thomas Witkowski's avatar
Thomas Witkowski committed
609
      // Test if the current row DOF is a periodic DOF.
610
      bool periodicRow = perMap.isPeriodic(rowFe, globalRowDof);
611

Thomas Witkowski's avatar
Thomas Witkowski committed
612 613 614 615
      // Dirichlet rows can be set only be the owner ranks.
      if (dirichletRows.count(*cursor) && !((*interiorMap)[rowComp].isRankDof(*cursor)))
	continue;

Thomas Witkowski's avatar
Thomas Witkowski committed
616 617 618
      if (!periodicRow) {
	// === Row DOF index is not periodic. ===

619
	// Get PETSc's mat row index.
Thomas Witkowski's avatar
Thomas Witkowski committed
620
	int rowIndex = interiorMap->getMatIndex(rowComp, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
621 622 623 624 625 626 627 628

	cols.clear();
	values.clear();

	for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	     icursor != icend; ++icursor) {

	  // Global index of the current column index.
629
	  MultiIndex colMultiIndex;
Thomas Witkowski's avatar
Thomas Witkowski committed
630
	  if ((*interiorMap)[colComp].find(col(*icursor), colMultiIndex) == false)
631 632 633
	    continue;

	  int globalColDof = colMultiIndex.global;
Thomas Witkowski's avatar
Thomas Witkowski committed
634
	  // Test if the current col dof is a periodic dof.
635
	  bool periodicCol = perMap.isPeriodic(colFe, globalColDof);
636
	  // Get PETSc's mat col index.
Thomas Witkowski's avatar
Thomas Witkowski committed
637
	  int colIndex = interiorMap->getMatIndex(colComp, globalColDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
638 639 640 641 642 643 644

	  // Ignore all zero entries, expect it is a diagonal entry.
 	  if (value(*icursor) == 0.0 && rowIndex != colIndex)
 	    continue;

	  if (!periodicCol) {
	    // Calculate the exact position of the column index in the PETSc matrix.
Thomas Witkowski's avatar
Thomas Witkowski committed
645 646
 	    cols.push_back(colIndex);
 	    values.push_back(value(*icursor));
Thomas Witkowski's avatar
Thomas Witkowski committed
647 648 649 650 651
	  } else {
	    // === Row index is not periodic, but column index is. ===

	    // Create set of all periodic associations of the column index.
	    std::set<int> perAsc;
652 653 654
	    perMap.fillAssociations(colFe, globalColDof, 
				    meshDistributor->getElementObjectDb(), perAsc);

Thomas Witkowski's avatar
Thomas Witkowski committed
655 656 657 658 659 660 661 662 663
	    // Scale value to the number of periodic associations of the column index.
	    double scaledValue = 
	      value(*icursor) * pow(0.5, static_cast<double>(perAsc.size()));

	    
	    // === Create set of all matrix column indices due to the periodic ===
	    // === associations of the column DOF index.                       ===

	    vector<int> newCols;
664
	    perMap.mapDof(colFe, globalColDof, perAsc, newCols);
Thomas Witkowski's avatar
Thomas Witkowski committed
665
	    for (unsigned int i = 0; i < newCols.size(); i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
666
	      cols.push_back(interiorMap->getMatIndex(colComp, newCols[i]));
Thomas Witkowski's avatar
Thomas Witkowski committed
667 668 669 670 671
	      values.push_back(scaledValue);	      
	    }
	  }
	}

672
  	MatSetValues(getMatInterior(), 1, &rowIndex, cols.size(), 
Thomas Witkowski's avatar
Thomas Witkowski committed
673
  		     &(cols[0]), &(values[0]), ADD_VALUES);	
Thomas Witkowski's avatar
Thomas Witkowski committed
674 675 676 677 678 679 680 681 682 683 684 685 686 687
      } else {
	// === Row DOF index is periodic. ===

	// Because this row is periodic, we will have to add the entries of this 
	// matrix row to multiple rows. The following maps store to each row an
	// array of column indices and values of the entries that must be added to
	// the PETSc matrix.
	map<int, vector<int> > colsMap;
	map<int, vector<double> > valsMap;

	// Traverse all column entries.
	for (icursor_type icursor = begin<nz>(cursor), icend = end<nz>(cursor); 
	     icursor != icend; ++icursor) {
	  // Global index of the current column index.
Thomas Witkowski's avatar
Thomas Witkowski committed
688
	  int globalColDof = (*interiorMap)[colComp][col(*icursor)].global;
Thomas Witkowski's avatar
Thomas Witkowski committed
689 690 691 692 693 694 695 696 697

	  // Ignore all zero entries, expect it is a diagonal entry.
 	  if (value(*icursor) == 0.0 && globalRowDof != globalColDof)
 	    continue;

	  // === Add all periodic associations of both, the row and the column ===
	  // === indices to the set perAsc.                                    ===

	  std::set<int> perAsc;
698 699 700 701
	  perMap.fillAssociations(colFe, globalColDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
	  perMap.fillAssociations(rowFe, globalRowDof, 
				  meshDistributor->getElementObjectDb(), perAsc);
Thomas Witkowski's avatar
Thomas Witkowski committed
702 703 704 705 706 707 708 709 710 711

	  // Scale the value with respect to the number of periodic associations.
	  double scaledValue = 
	    value(*icursor) * pow(0.5, static_cast<double>(perAsc.size()));


	  // === Create all matrix entries with respect to the periodic  ===
	  // === associations of the row and column indices.             ===

	  vector<pair<int, int> > entry;
Thomas Witkowski's avatar
Blbu  
Thomas Witkowski committed
712 713
	  perMap.mapDof(rowFe, colFe, make_pair(globalRowDof, globalColDof),
			perAsc, entry);
Thomas Witkowski's avatar
Thomas Witkowski committed
714 715 716

	  // === Translate the matrix entries to PETSc's matrix.

717
	  for (unsigned int i = 0; i < entry.size(); i++) {
Thomas Witkowski's avatar
Thomas Witkowski committed
718 719
	    int rowIdx = interiorMap->getMatIndex(rowComp, entry[i].first);
	    int colIdx = interiorMap->getMatIndex(colComp, entry[i].second);
Thomas Witkowski's avatar
Thomas Witkowski committed
720

721 722
	    colsMap[rowIdx].push_back(colIdx);
	    valsMap[rowIdx].push_back(scaledValue);
Thomas Witkowski's avatar
Thomas Witkowski committed
723 724 725 726 727 728 729 730 731 732 733 734
	  }
	}


	// === Finally, add all periodic rows to the PETSc matrix. ===

	for (map<int, vector<int> >::iterator rowIt = colsMap.begin();
	     rowIt != colsMap.end(); ++rowIt) {
	  TEST_EXIT_DBG(rowIt->second.size() == valsMap[rowIt->first].size())
	    ("Should not happen!\n");

	  int rowIndex = rowIt->first;
735

736
	  MatSetValues(getMatInterior(), 1, &rowIndex, rowIt->second.size(),
Thomas Witkowski's avatar
Thomas Witkowski committed
737 738 739 740 741 742 743
		       &(rowIt->second[0]), &(valsMap[rowIt->first][0]), ADD_VALUES);
	}
      }
    }
  }


Thomas Witkowski's avatar
Thomas Witkowski committed
744 745
  void PetscSolverGlobalMatrix::setDofVector(Vec vecInterior, 
					     Vec vecCoarse,
746
					     DOFVector<double>* vec, 
Thomas Witkowski's avatar
Thomas Witkowski committed
747
					     int rowComp, 
748
					     bool rankOnly)
Thomas Witkowski's avatar
Thomas Witkowski committed
749 750 751
  {
    FUNCNAME("PetscSolverGlobalMatrix::setDofVector()");

752
    const FiniteElemSpace *feSpace = vec->getFeSpace();
753
    PeriodicMap &perMap = meshDistributor->getPeriodicMap();
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
754

755
    ParallelDofMapping *rowCoarseSpace = 
Thomas Witkowski's avatar
Thomas Witkowski committed
756 757 758
      (coarseSpaceMap.size() ? coarseSpaceMap[rowComp] : NULL);

    map<DegreeOfFreedom, double> &dirichletValues = vec->getDirichletValues();
759

Thomas Witkowski's avatar
Thomas Witkowski committed
760 761 762
    // Traverse all used DOFs in the dof vector.
    DOFVector<double>::Iterator dofIt(vec, USED_DOFS);
    for (dofIt.reset(); !dofIt.end(); ++dofIt) {
Thomas Witkowski's avatar
Thomas Witkowski committed
763 764 765 766 767
      
      DegreeOfFreedom dof = dofIt.getDOFIndex();
      
      if (rankOnly && !(*interiorMap)[rowComp].isRankDof(dof))
	continue;
768

769 770
      bool isCoarseDof = isCoarseSpace(rowComp, dof);

Thomas Witkowski's avatar
Thomas Witkowski committed
771
      // Dirichlet rows can be set only be the owner ranks.
772 773 774 775 776
      if (dirichletValues.count(dof)) {
	if ((!isCoarseDof && !((*interiorMap)[rowComp].isRankDof(dof))) ||
	    (isCoarseDof && !((*rowCoarseSpace)[rowComp].isRankDof(dof))))
	  continue;
      }
Thomas Witkowski's avatar
Thomas Witkowski committed
777

778
      if (isCoarseDof) {
779 780
	TEST_EXIT_DBG(vecCoarse != PETSC_NULL)("Should not happen!\n");

Thomas Witkowski's avatar
Thomas Witkowski committed
781
	int index = rowCoarseSpace->getMatIndex(rowComp, dof);
782 783
	VecSetValue(vecCoarse, index, *dofIt, ADD_VALUES);
      } else {
Thomas Witkowski's avatar
Thomas Witkowski committed
784
	if ((*interiorMap)[rowComp].isSet(dof) == false)
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
785 786
	  continue;

787
	// Calculate global row index of the DOF.
Thomas Witkowski's avatar
Thomas Witkowski committed
788
	DegreeOfFreedom globalRowDof = (*interiorMap)[rowComp][dof].global;
789 790 791 792 793
	
	// Get PETSc's mat index of the row DOF.
	int index = 0;
	if (interiorMap->isMatIndexFromGlobal())
	  index = 
Thomas Witkowski's avatar
Thomas Witkowski committed
794
	    interiorMap->getMatIndex(rowComp, globalRowDof) + rStartInterior;
795 796
	else
	  index =
Thomas Witkowski's avatar
Thomas Witkowski committed
797
	    interiorMap->getMatIndex(rowComp, dof) + rStartInterior;
798

799
	if (perMap.isPeriodic(feSpace, globalRowDof)) {
Thomas Witkowski's avatar
Thomas Witkowski committed
800 801 802
	  std::set<int>& perAsc = perMap.getAssociations(feSpace, globalRowDof);
	  double value = *dofIt / (perAsc.size() + 1.0);
	  VecSetValue(vecInterior, index, value, ADD_VALUES);
803

Thomas Witkowski's avatar
Thomas Witkowski committed
804 805 806
	  for (std::set<int>::iterator perIt = perAsc.begin(); 
	       perIt != perAsc.end(); ++perIt) {
	    int mappedDof = perMap.map(feSpace, *perIt, globalRowDof);
Thomas Witkowski's avatar
Thomas Witkowski committed
807
	    int mappedIndex = interiorMap->getMatIndex(rowComp, mappedDof);
808

Thomas Witkowski's avatar
Thomas Witkowski committed
809
	    VecSetValue(vecInterior, mappedIndex, value, ADD_VALUES);
810 811 812
	  }	  
	} else {	  
	  // The DOF index is not periodic.
Thomas Witkowski's avatar
Thomas Witkowski committed
813 814
	  VecSetValue(vecInterior, index, *dofIt, ADD_VALUES);
	}
Thomas Witkowski's avatar
Thomas Witkowski committed
815 816 817 818
      }
    }
  }

819 820 821 822 823 824 825 826 827 828

  PetscSolver* PetscSolverGlobalMatrix::createSubSolver(int component,
							string kspPrefix)
  {
    FUNCNAME("PetscSolverGlobalMatrix::createSubSolver()");

    vector<const FiniteElemSpace*> fe;
    fe.push_back(componentSpaces[component]);

    PetscSolver* subSolver = new PetscSolverGlobalMatrix("");
829
    subSolver->setKspPrefix(kspPrefix);
830
    subSolver->setMeshDistributor(meshDistributor, 0);
831 832 833 834 835 836 837 838 839
    subSolver->init(fe, fe);

    ParallelDofMapping &subDofMap = subSolver->getDofMap();
    subDofMap[0] = dofMap[component];
    subDofMap.update();

    return subSolver;
  }

840 841 842 843

  void PetscSolverGlobalMatrix::setConstantNullSpace(KSP ksp,
						     int constFeSpace,
						     bool test)
Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866
  {
    FUNCNAME("PetscSolverGlobalMatrix::setConstantNullSpace()");

    Vec nullSpaceBasis;
    VecDuplicate(getVecSolInterior(), &nullSpaceBasis);
    
    SystemVector basisVec("tmp", componentSpaces, componentSpaces.size(), true);
    basisVec.set(0.0);
    basisVec.getDOFVector(constFeSpace)->set(1.0);
    
    setDofVector(nullSpaceBasis, basisVec, true);
    VecAssemblyBegin(nullSpaceBasis);
    VecAssemblyEnd(nullSpaceBasis);
    VecNormalize(nullSpaceBasis, PETSC_NULL);
    
    if (test) {
      Vec tmp;
      MatGetVecs(getMatInterior(), &tmp, PETSC_NULL);
      MatMult(getMatInterior(), nullSpaceBasis, tmp);
      PetscReal n;
      VecNorm(tmp, NORM_2, &n);
      MSG("NORM IS: %e\n", n);
      VecDestroy(&tmp);
867
    }
Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
868 869 870
    
    
    MatNullSpace matNullSpace;
871
    MatNullSpaceCreate(domainComm, PETSC_FALSE, 1, &nullSpaceBasis, &matNullSpace);
Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
872 873 874 875
    KSPSetNullSpace(ksp, matNullSpace);
    MatNullSpaceDestroy(&matNullSpace);
  }

876

Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
877 878 879 880 881
  void PetscSolverGlobalMatrix::setConstantNullSpace(KSP ksp)
  {
    FUNCNAME("PetscSolverGlobalMatrix::setConstantNullSpace()");

    MatNullSpace matNullSpace;
882
    MatNullSpaceCreate(domainComm, PETSC_TRUE, 0, PETSC_NULL, &matNullSpace);
Thomas Witkowski's avatar
blub  
Thomas Witkowski committed
883 884 885
    KSPSetNullSpace(ksp, matNullSpace);
    MatNullSpaceDestroy(&matNullSpace);
  }
886

Thomas Witkowski's avatar
Thomas Witkowski committed
887
}